You can batch render your render targets. In addition, you can use the Renderable flag on each render pass, render layer, or render target's Attribute Editor to determine whether it is also included in the batch render.
To include a render pass or render target or render layer in your batch render
You can also choose to perform only a 2D render or only a 3D render, or to do both.
To batch render only your render targets (2D) or the dependencies (3D)
By selecting All Renderable, all renderable dependencies and render targets are included in the batch render. Select Render Targets Only to perform a 2D render and render only the render targets. This option is ideal if you are satisified with your 3D renders and you are only tweaking your composite. Select Omit Render Targets to perform a 3D render and render only the renderable dependencies.
You can use command line rendering to perform your batch render. Render flags that are the equivalent of the options: All Renderable, Render Targets Only, and Omit Render Targets are available. See Render from the command line and mental ray for Maya renderer command line renderer flags for more information.
After selecting Render > Batch Render, a separate folder is created for each render layer in your images directory. Your render target output is saved to the masterLayer folder if its renderLayer input is either not connected, or connected to the masterLayer (in other words, defaultRenderLayer). If you've connected a different render layer to the render target renderLayer input, then the render target output is saved to the folder for that layer.
Rendered image filename options
Use render tokens to customize the filenames of your render output. Use the <RenderPass> token to add your render target name to the created subfolder or image file name.
For instance, in the example above, using a Filename prefix of <RenderLayer>\<RenderPass>\ will create separate folders for each render layer as well as separate folders for each render pass and the render target. The render target folder is saved to the masterLayer folder.